char2TreeCategorical: Creates a categorical trait tree from a set of tip species.

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Creates a categorical trait tree from a set of tip species.

Description

Creates a categorical trait tree from a set of tip species.

Usage

char2TreeCategorical(
  tipvals,
  treesObj,
  useSpecies = NULL,
  model = "ER",
  root_prior = "auto",
  plot = FALSE,
  anctrait = NULL
)

Arguments

tipvals	the trait/phenotype/character value at the tip, names(tip.vals) should match some of the mastertree$tip.label, though a perfect match is not required
treesObj	A treesObj created by readTrees
useSpecies	Give only a subset of the species to use for ancestral state reconstruction (e.g., only those species for which the trait can be reliably determined).
model	Specifies what rate model to use
root_prior	The prior probabilities of each trait at the root used to fit the transition matrix. Can be a vector of length equal to the number of states or one of the following: "flat", "empirical", "stationary", "likelihoods", "max_likelihood".
plot	Plots a phenotype tree
anctrait	The trait to use for all ancestral species instead of inferring ancestral states if not NULL. The default is NULL.

Value

A tree with edge.length representing phenotype states

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.